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The Arabidopsis genome was initially annotated by the Arabidopsis Genome Initiative (AGI) and later reannotated by TIGR in collaboration with MIPS and TAIR. TAIR assumed primary responsibility for maintaining the Arabidopsis genome annotation in North America following TIGR's final release (TIGR5), producing 5 additional genome releases, TAIR6 through TAIR10. TAIR10 was integrated into GenBank in November 2010.
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- 227 single nucleotide substitutions were made to the assembly sequence based on re-sequencing data provided by Richard Clark (Ossowski et al. 2008) and Joe Ecker.
- 341 indels were made to the assembly sequence based on re-sequencing data provided by Richard Clark and EST and cDNA sequences deposited in Genbank that supported the insertion/deletion.
- 14 regions previously identified in TAIR8 as either vector, E.coli or rice contamination, and where the existing sequence had been substituted with the equivalent number of IUPAC ambiguity code 'N's were standardized (via deletion) to a set size of 100bp.
- All five nuclear chromosomes were updated for TAIR9 details of the golden path length of each chromosome can be found at here.
Further details of these TAIR 9 assembly changes and earlier TAIR8 updates can be found at ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/ Assembly updates and gap information can also be viewed in TAIRs GBrowse (see Assembly tracks section) are linked.
We would like to thank all those who contributed to the latest release by providing submissions for new and incorrectly annotated genes. TAIR wishes to thank Cornell University for use of the computer clusters at the Cornell Center for Advanced Computing (CAC).
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The fully annotated chromosome sequences in TIGR xml format or GFF format, along with Fasta FASTA files of cDNA, CDS, genomic and protein sequences, and lists of added, deleted and updated genes are available from the TAIR ftp Download site.
Previous TIGR annotation is available from both the TIGR FTP site and TAIR FTP TAIR Download site.
For a summary of the different genome version statistics see table All Genome Versions Statistics below.
Fasta FASTA formatted files for all TAIR sequence analysis datasets including sets of intron, intergenic, UTR, upstream and downstream sequences are also available in the blast BLAST datasets directory of the TAIR Download Section.
Datasets are also available from TAIR's Bulk Download tool Advanced Gene Search; paste in or upload a list of AGI identifiers (such as At1g01010) and download the corresponding sequences. A graphic display of the Arabidopsis sequence and annotation can be viewed using TAIR's genome browsers GBrowse and Seqviewer.
Transposon genes and Transposable elements
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Transposable element annotations provided by Hadi Quesneville were combined with pre-existing annotations to create a composite set of Arabidopsis transposons. These have been assigned a unique identifier (e.g. AT3TE53245) that indicates relative position on the chromosome. Under defined criteria (see additional readme-transposons) we have associated transposons to overlapping transposable element genes e.g. genes AT3G32022, AT3G32024, AT3G32026, AT3G32027 and AT3G32028 are associated to transposon AT3TE53245. Transposons can be viewed in TAIR's GBrowse genome browsers and additional information can be found on the Transposon and Transposon family detail pages.
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| Protein Coding Genes | Transposons and pseudogenes | Alternatively spliced genes | Gene density (Kb/gene) | Avg. exons per gene | Avg. exon length | Avg. intron length | |
|---|---|---|---|---|---|---|---|
| Araport11 (06/16) | 27,655 | 4,853 | 10,695 | 6.7 | 335.5 | ||
| TAIR10 (11/10) | 27,411 | 4,827 | 5,885 | 4.35 | 5.89 | 296 | 165 |
| TAIR9 (6/09) | 27,379 | 4,827 | 4,626 | 4.35 | 5.67 | 304 | 165 |
| TAIR8 (4/08) | 27,235 | 4,759 | 4,330 | 4.37 | 5.62 | 306 | 165 |
| TAIR7 (4/07) | 26,819 | 3,889 | 3,866 | 4.44 | 5.79 | 268 | 165 |
| TAIR6 (11/05) | 26,541 | 3,818 | 3,159 | 4.48 | 5.64 | 269 | 164 |
| TIGR5 (1/04) | 26,207 | 3,786 | 2,330 | 4.54 | 5.42 | 276 | 164 |
| TIGR4 (4/03) | 27,170 | 2,218 | 1,267 | 4.38 | 5.31 | 279 | 166 |
| TIGR3 (8/02) | 27,117 | 1,967 | 162 | 4.32 | 5.24 | 266 | 166 |
| TIGR2 (1/02) | 26,156 | 1,305 | 28 | 4.48 | 5.25 | 265 | 167 |
| TIGR1 (8/01) | 25,554 | 1,274 | 0 | 4.55 | 5.23 | 256 | 168 |
| Nature (12/00) | 25,498 | NA | NA | 4.50 | 5.20 | 250 | 168 |
Graphical Views of Annotation Data
TAIR GBrowse
Search or browse a map of the Arabidopsis genome (including genes, cDNAs and ESTs, insertion mutants, SNPs, markers, BACs, VISTA sequence similarity plots and more) or upload your own annotation track. Tracks can be easily customized by turning on and off specific data types, collapsing and expanding tracks, or changing track order.
TAIR SeqViewer
A graphic display of the latest Arabidopsis sequence and annotation can be viewed using TAIRs genome browser. Browse the chromosomes, search for names or short sequences and view search hits on the whole genome, in a close-up view or on a nucleotide level.
TAIR MapViewer
Displays ORFs at zoom levels of 200x and higher, and allows wildcard and alias searching on clone names, ORF names, genes and markers.
NCBI Map Viewer
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